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WO2018134346A9 - Spectrométrie de masse à gamme dynamique améliorée - Google Patents

Spectrométrie de masse à gamme dynamique améliorée Download PDF

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Publication number
WO2018134346A9
WO2018134346A9 PCT/EP2018/051290 EP2018051290W WO2018134346A9 WO 2018134346 A9 WO2018134346 A9 WO 2018134346A9 EP 2018051290 W EP2018051290 W EP 2018051290W WO 2018134346 A9 WO2018134346 A9 WO 2018134346A9
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regions
ion
mass
interest
ions
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PCT/EP2018/051290
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English (en)
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WO2018134346A1 (fr
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Matthias Mann
Jürgen COX
Florian Meier
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MAX-PLANCK-Gesellschaft zur Förderung der Wissenschaften e.V.
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Publication of WO2018134346A1 publication Critical patent/WO2018134346A1/fr
Publication of WO2018134346A9 publication Critical patent/WO2018134346A9/fr

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    • H—ELECTRICITY
    • H01—ELECTRIC ELEMENTS
    • H01J—ELECTRIC DISCHARGE TUBES OR DISCHARGE LAMPS
    • H01J49/00—Particle spectrometers or separator tubes
    • H01J49/0027—Methods for using particle spectrometers
    • H—ELECTRICITY
    • H01—ELECTRIC ELEMENTS
    • H01J—ELECTRIC DISCHARGE TUBES OR DISCHARGE LAMPS
    • H01J49/00—Particle spectrometers or separator tubes
    • H01J49/26—Mass spectrometers or separator tubes
    • H01J49/34—Dynamic spectrometers
    • H01J49/42—Stability-of-path spectrometers, e.g. monopole, quadrupole, multipole, farvitrons
    • H01J49/426—Methods for controlling ions
    • H01J49/4265—Controlling the number of trapped ions; preventing space charge effects

Definitions

  • the present invention relates to a method of mass spectrometry (MS) comprising: (a) partitioning an mass-to-charge ( m/z ) range of interest in two or more regions; (b) defining at least two sets of regions, each set of regions consisting of at least one region as defined in step (a), provided that all sets of regions, when taken together, cover said m/z range in its entirety; (c) ionizing a sample of interest and storing (a) defined number(s) of ions for each region of a given set of regions, thereby obtaining one or more ion populations; (d) combining, if applicable, the more than one ion populations of (c); (e) analyzing the one ion population obtained in step (c) or the combined ion populations obtained in step (d), respectively, in a detector, thereby obtaining a partial mass spectrum; and (f) repeating steps (c) to (e) for each set of regions.
  • MS mass spectrometry
  • Mass spectrometers that trap ions are an important segment of the overall market and they dominate the proteomics market in particular.
  • Examples for this type of mass spectrometers include, not exclusively, quadrupole-ion trap, quadrupole-Fourier transform ion cyclotron resonance, linear ion trap-Orbitrap and quadrupole-Orbitrap instruments. They are very powerful but an inherent limitation is that the number of ions that can be simultaneously stored in an ion trapping device is limited by space charge effects. Exceeding the space charge limit has deleterious effects on the quantitative accuracy, as well as mass resolution and mass accuracy when the trapping device is employed as a mass analyzer. To achieve an optimal performance of the ion trap, it is therefore necessary to control the number of stored ions.
  • AGO automatic gain control
  • the median ion injection times for full scans are typically ⁇ 1 ms; less than 0.8 % of the required transient time for a spectrum at a mass resolution of 60,000 at m/z 200 with the high-field Orbitrap cell (128 ms); see, for example, Scheltema, R. A. et al.
  • the ion current in particular in the analysis of complex compound mixtures, is typically concentrated on a few mass-to-charge channels rather than evenly distributed across the full scan.
  • the described limitations of full scans in terms of dynamic range and sensitivity can be partially overcome by focusing the analysis on a narrow m/z range, which is a fraction of the initial m/z range of interest.
  • This is commonly applied in targeted quantification assays, for instance‘single ion monitoring’, in which a quadrupole mass filter selects a narrow mass window prior to the trapping device and thus excludes high abundant interferences.
  • WO 2014/200987 describes MS involving gas-phase enrichment using notched isolation waveforms.
  • the method described in this document involves simultaneous entry of all ions to be analyzed into the ion trap. A mass filter which would allow partitioning of the m/z range is not applied.
  • Improvements preferably address the acquisition of full scans and include better signal-to-noise ratio, more efficient use of the incoming ion beam and increased dynamic range.
  • the present invention relates to a method of mass spectrometry (MS) comprising: (a) partitioning an m/z range of interest in two or more regions; (b) defining at least two sets of regions, each set of regions consisting of at least one region as defined in step (a), provided that all sets of regions, when taken together, cover said m/z range in its entirety; (c) ionizing a sample of interest and storing (a) defined number(s) of ions for each region of a given set of regions, thereby obtaining one or more ion populations; (d) combining, if applicable, the more than one ion populations of (c); (e) analyzing the one ion population obtained in step (c) or the combined ion populations obtained in step (d), respectively, in a detector, thereby obtaining a partial mass spectrum; and (f) repeating steps (c) to (e) for each set of regions.
  • MS mass spectrometry
  • mass spectrometry has its art-established meaning. In particular, it relates to an analytical method that ionizes chemical compounds and sorts the obtained ions based on their mass-to-charge (m/z) ratio.
  • a common unit of the mass-to- charge ratio is Thomson (Th).
  • the information acquired in a mass spectrometer can be depicted and stored as a mass spectrum.
  • a mass spectrum is a diagram or table, or, in computational terms, an array, where for any given m/z value of interest, the ion abundance is given. Assuming that peaks in the mass spectrometer would not coincide or overlap, a non zero abundance at a given m/z value is a measure of the abundance of a specific ion species.
  • the term“abundance” is generally understood as designating the amount of a specific chemical species.
  • the number (as opposed to abundance) of ions acquired or stored in an ion store is an important parameter.
  • a“number of ions” this is generally understood as not being specific for a particular chemical species. Rather, it is the total number of ions, irrespective of the underlying chemical nature, which has been acquired in a given time interval or is being stored in an ion store.
  • Step (a) of the method in accordance with the first aspect of the present invention provides for partitioning or dividing a given m/z range of interest in two or more regions.
  • the m/z range of interest is preferably contiguous.
  • said regions in their entirety cover the entire m/z range of interest.
  • the regions resulting from the partitioning in accordance with step (a) are assigned to sets of regions. Each of the regions is assigned to a set of regions. As a consequence, all sets of regions, when taken together, cover said m/z range in its entirety.
  • Regions and set of regions are illustrated in an exemplary manner in Figure 1.
  • the three graphs being designated first boxcar scan, second boxcar scan and third boxcar scan each depict a set of regions, wherein each set of regions consists of four regions.
  • the particular shape of the ion transmission function depicted in Figure 1 is preferred, but not limiting. More specifically, in Figure 1 , each region is defined by a boxcar function.
  • a boxcar function is a function which is zero or the entire real-line except for a single interval where it is equal to a constant. In the exemplary implementation depicted in Figure 1 , said constant is 100% ion transmission.
  • the uppermost part of Figure 1 depicts the standard acquisition scheme of a full scan in a mass spectrometer.
  • a sample of interest is ionized and ions for each region of a given set of regions is stored.
  • Ions corresponding to different regions within said given set of regions may be stored in distinct ion stores. Preferred is that they are stored in the same ion store or, equivalently, accumulated in said same ion store.
  • ions for each region of a given set of regions are selected sequentially (timewise) and stored.
  • Preferred methods of ionizing include for example electrospray ionization, nano-electrospray ionization, chemical ionization, atmospheric pressure chemical ionization, atmospheric pressure photoionization and matrix-assisted laser desorption ionization.
  • Step (d) provides for combining the ion populations of (c) for those implementations where at least one set of regions consists of more than one region. To the extent a set of regions consists of only one region (which is not preferred), step (d) is dispensable.
  • the method of the invention also includes (less preferred) implementations where ions from different regions of a set of regions are stored in different ion stores and subsequently combined in step (d).
  • a mass spectrometer that could be used for this implementation is disclosed in US 2010-0314538-A1.
  • step (e) the method in accordance with the first aspect proceeds, in accordance with step (e), to analyzing them in the detector of the mass spectrometer.
  • step (f) Said mass analyzing is also referred to as“scan” herein.
  • scans in accordance with the invention are also referred to as“boxcar scans”.
  • a preferred implementation of the methods in accordance with the first aspect provides for accumulating the ion populations originating from the regions of a set of regions in a single ion store.
  • Such preferred implementation is as follows: a method of mass spectrometry (MS) comprising: (a) partitioning an m/z range of interest in two or more regions; (b) defining at least two sets of regions, each set of regions consisting of at least one region as defined in step (a), provided that all sets of regions, when taken together, cover said m/z range in its entirety; (c) ionizing a sample of interest and storing (a) defined number(s) of ions for each region of a given set of regions, thereby obtaining one or more ion populations; (d) accumulating, if applicable, the more than one ion populations of (c); (e) analyzing the one ion population obtained in step (c) or the accumulated ion populations obtained in step (d),
  • each set of regions consists of at least two regions.
  • a further preferred implementation of the method in accordance with the first aspect is as follows: a method of mass spectrometry (MS) comprising: (a) partitioning an m/z range of interest in four or more regions; (b) defining at least two sets of regions, each set of regions consisting of at least two regions as defined in step (a), provided that all sets of regions, when taken together, cover said m/z range in its entirety; (c) ionizing a sample of interest and storing (a) defined number(s) of ions for each region of a given set of regions, thereby obtaining two or more ion populations; (d) accumulating the two more ion populations of (c); (e) analyzing the accumulated ion populations obtained in step (d) in a detector, thereby obtaining a partial mass spectrum; and (f) repeating steps (c) to (e) for each set of regions.
  • MS mass spectrometry
  • the method in accordance with the first aspect further comprises (g) combining the mass spectra obtained in steps (e) and (f), thereby obtaining a combined mass spectrum of said m/z range of interest.
  • the method in accordance with the first aspect provides for improved signal-to-noise ratio (S/N), greater dynamic range, and more efficient use of the incoming ion beam.
  • S/N signal-to-noise ratio
  • a much larger proportion (up to 10-fold or more) of the incoming ion current is used for mass analysis and quantification.
  • Partitioning in accordance with step (a) of the method of the first aspect may be data- dependent or data-independent.
  • An example of data-independent partitioning is a simple division of the m/z range of interest by the number of regions. If the number of regions is n, the size of each region will then be the n-th part of the m/z range of interest. While overall a significant number of low abundant species will benefit from such data-independent partition scheme, it cannot be excluded that in a given region there is a highly abundant species and a very low abundant species, the low abundant species being of particular interest. Owing to the presence of the highly abundant species in the same region, the low abundant species might still escape detection. One approach of dealing with this situation is to increase the number of regions.
  • partitioning may be effected such that highly abundant species become assigned to regions which are narrow on the m/z axis, the consequence being that the abundant species is practically the only species present in such a tailored region.
  • Low abundant species of interest even if they would be close to the mentioned highly abundant species on the m/z axis would end up in adjacent regions, where more ion injection time would be dedicated to them.
  • the total ion injection time spent will in general exceed by far the injection time used in a standard full scan, assuming that in either case the same total number of ions (such as 3 x 10 6 ) would be analyzed. Yet, this can be easily accommodated within the normal duty cycle of the mass spectrometer. Typically 64, 128 or 256 milliseconds are spent for the acquisition of a full mass spectrum. These values refer to the current generation of Orbitrap mass analyzers.
  • the invention also applies to other detectors, for example linear ion traps, 3D ion traps, time- of-flight or FT-ICR mass analyzers.
  • step (g) Owing to the fact that in (almost) any case more ion injection time is dedicated to less abundant species, a raw combined mass spectrum obtained in step (g) will generally show low abundance species artificially overrepresented. Given that the ion injection time spent in each region is known, this can be accounted for. Said accounting for is subject of a preferred embodiment and of a separate aspect drawn to a computational method which are also part of this invention and will be disclosed and discussed further below.
  • said defined number of ions is the same for each of said regions; and/or (ii) the total number of ions is the same for each set of regions.
  • the sum of the defined numbers of ions, said sum being over all regions in a given set of regions, does not exceed the total ion capacity of said ion store and/or said detector; and/or (ii) is less or equal about 5 x 10 5 , preferably less or equal about 10 6 , and more preferably less or equal about 3 x 10 6 .
  • said defined number of ions is the same for each region and (i) does not exceed the total ion capacity of said ion store and/or of said detector divided by the number of regions per set of regions; and/or (ii) is less or equal about 10 5 .
  • the above preferred embodiments account for inherent limitations of ion stores and detectors in that beyond the space charge limit, accuracy and precision decrease.
  • a consensus value at present and valid, for example, for the mass spectrometer shown in Figure 5, is three million ions. In a given scan in accordance with the present invention, that value should not be exceeded. Accordingly, the above preferred embodiment limits the number of ions originating from all regions of a given set of regions to less or equal about 3 x 10 6 .
  • the maximum ion injection time may be used as an additional parameter to restrict the analysis time in cases where the target number of ions is not reached within a reasonable time and waiting for the total ion number criterion as defined above being met would lower throughput of the spectrometer.
  • a double criterion of a maximum for the sum of the defined numbers of ions plus a maximum ion injection time the latter being, e.g. between about 50 ms and about 200 ms.
  • An exemplary double criterion would be to fill the C-trap with a maximum of 3 x 10 6 ions in maximum of 100 ms. Such double criterion ensures a high duty cycle of the Orbitrap mass analysis.
  • said sets of regions are interleaved on the m/z axis.
  • two regions which are adjacent on the m/z axis do not belong to the same set of regions.
  • An example of these interleaved sets of regions is shown in Figure 1.
  • regions belonging to the first set and regions belonging to the second set alternate along the m/z axis in accordance with this embodiment.
  • the number of sets of regions is 2, 3, 4, 5 or more, preferably 2, more preferably 3; and/or (ii) the number of regions per set of regions is independently for each set of regions 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13, 14, 15 or more, preferably 12.
  • said regions in each set of regions are interspaced on the m/z axis. Accordingly, to the extent a set of regions consists of more than one region, two neighboring regions within a given set of regions are never adjacent on the m/z axis. Any intervening region or intervening regions belong to one or more different sets of regions. This is illustrated in Figure 1.
  • Preferred analytes comprised in the sample of interest are one, more or all of peptides, polypeptides, proteins, lipids, carbohydrates, nucleic acids, oligonucleotides and metabolites. Particularly preferred are peptides as they are obtained by an enzymatic digest of one or more proteins. Preferred implementations of said “one or more proteins” are entire proteomes. Preferred enzymes for enzymatic digestion include trypsin and Lys-C.
  • said m/z range is from about 100 to about 2000 Th, preferably from about 300 to about 1650 Th, about 400 to about 1200 Th, or about 500 to about 1000 Th.
  • said regions are of equal size; or (i-2) the size of said regions depends on the m/z value and/or the ion current, preferably in real time; and/or (ii) the number of regions in each set of regions is equal.
  • the expected m/z distribution of the obtained tryptic peptides is, at least approximately, known in advance. In other words, it is known in advance how the ion beam will behave, in a quantitative sense, as a function of m/z. In LC- MS experiments, the behavior of the ion beam can also be superimposed by a function of the retention time.
  • a standard scan of the m/z range of interest may be performed beforehand in order to acquire knowledge of the location of the most abundant species. Such scan is subject of the preferred embodiment; see step (h) as described further below.
  • regions may be specifically tailored to those most abundant species such that each region comprising a given abundant species is very narrow on the m/z axis. Such narrow regions may have width of less or equal 10 Th, less or equal 8 Th, less or equal 4 Th, less or equal 3 Th, less or equal 2 Th, less or equal 1.4 Th, or less or equal 1 Th.
  • Either type of knowledge can be used to implement a dependency of the size of said regions on the m/z value.
  • the ion current may be measured in real-time as a means of controlling ion transmission and/or region size.
  • adjacent regions overlap, preferably by about 0.1 to about 10 Th, more preferably about 1 Th.
  • Adjacent regions are regions which are contiguous on the m/z axis. In view of the preferred embodiments disclosed above, such adjacent regions preferably belong to different sets of regions.
  • said partitioning is effected in a mass filter, preferred mass filters being quadrupole and linear ion trap;
  • said storing is effected in at least one ion store, preferred ion stores being C-trap and linear ion trap; and/or
  • said analyzing is effected in at least one detector, preferred detectors being Orbitrap mass analyzer, time-of-flight mass analyzer, 3D ion trap, linear ion trap and FT-ICR; wherein said mass filter, said ion store(s) and said detector(s) are comprised in (a) mass spectrometer(s).
  • mass filter particular preference is given to a quadrupole mass filter.
  • filling of the ion store(s) is controlled by an automatic gain control (AGC) algorithm.
  • AGC automatic gain control
  • the AGC algorithm is known in the art and explained in the introductory section.
  • each region is defined by an ion transmission function which is a boxcar function of m/z.
  • the constant value of the boxcar function is 100% ion transmission.
  • boxcar functions defining adjacent regions overlap, preferably by about 0.1 to about 10 Th, more preferably about 1 Th.
  • the term “boxcar function” is defined herein above.
  • Figure 1 displays each scan in accordance with the present invention as a series as boxcar functions. By definition, boxcar functions are rectangular in shape when plotted. A set of regions may accordingly be represented as a series of boxcar functions; see Figure 1.
  • the method in accordance with the first aspect of the invention further comprises (h) analyzing, in the absence of prior partitioning, all ions in said m/z range of interest. This step is preferably performed prior to step (c).
  • Step (h) is a standard full scan of the given m/z interval of interest. It is depicted in the upper part of Figure 1. Given that this is the art-established standard scan, it will suffer from the deficiencies discussed herein above, i.e. worse signal-to-noise ratio, especially of low abundant ion species, as compared to the method of the present invention. Yet, step (h) can be employed for post-processing of the combined mass spectrum obtained in step (g). Said post-processing is subject of a separate aspect of the present invention, namely the computational method discussed further below. A key aspect of said processing is subject of the following preferred embodiment.
  • step (h) can be equal to or wider than the range covered by boxcar scans.
  • full scan m/z 300-1650; all boxcar scans combined: m/z 400-1000.
  • the method in accordance with the first aspect further comprises determining the effective transmission efficiency of the mass filter by comparing ion abundances observed in steps (e), (f) and/or (g) with those observed in step (h).
  • the combined mass spectrum as obtained in step (g), while improving S/N for low abundant species and improving dynamic range, will generally, from a quantitative perspective, be characterized by an overrepresentation of low abundant species.
  • the combined mass spectrum of step (g) can be readjusted to properly reflect the quantities as they occur in the sample of interest. Such readjustment, notably, does not lead to a deterioration of the signal-to-noise ratio which in accordance with the invention is significantly improved when compared to a standard scan in accordance with step (h).
  • step (a) for example by means of boxcar functions is not perfect.
  • a real boxcar function may be characterized by edge effects in that close to the boundaries of the boxcar function the ion transmission drops below 100%. Also this can be corrected by the mentioned readjusting, said readjusting using the information from the scan performed in accordance with step (h).
  • step (h) can also be used for obtaining information about the overall shape of the spectrum in the m/z range of interest, in particular about locations of the most abundant species. This information in turn can then be used for a data-dependent partitioning of the m/z range in regions.
  • a preceding boxcar scan instead of a conventional full scan
  • m/z regions with low ion current may be combined in one larger region.
  • said sample of interest is the eluate of a chromatography device, said chromatography device preferably being coupled online to said mass spectrometer.
  • chromatography is liquid chromatography (LC) or gas chromatography (GC).
  • said method further comprises, after step (f), (g) or (h), performing fragment ion scans of one or more precursor ion species of interest, wherein said precursor ion species is/are selected from (i) the mass spectrum obtained in step (h); (ii) a partial mass spectrum obtained in step (e); and/or (iii) the combined mass spectrum obtained in step (g).
  • fragment ion scan refers to a particular operation mode of the mass spectrometer.
  • the primary ions obtained upon ionizing in accordance with step (c) are subjected to fragmentation.
  • said primary ions are also referred to as“precursor ions”.
  • fragment ion scans are performed (i) separately for each one of said one or more precursor ion species; or (ii) for more than one precursor ion species or all precursor ion species of interest simultaneously.
  • fragment ion scans may be performed in a data-independent way.
  • precursor ions of interest are either chosen in data-dependent manner, e.g. ions are ranked by their relative abundance (topN method), or can also be specified in a‘target list’.
  • said method further comprises, after step (f), (g) or (h), performing one or more fragment ion scans (MS2 scans) across an m/z range of interest, preferably using one or more data-independent m/z selection window(s).
  • MS2 scans fragment ion scans
  • data-independent acquisition refers to a method that performs a plurality of fragment ion scans one or more times in a single experiment across a mass range using a plurality of pre-determined, i.e., data-independent mass selection windows. These windows are typically broader than those used for data-dependent methods, noting that data- dependent methods typically focus on peaks of interest.
  • the present invention can advantageously be combined with data-independent acquisition to extend the library strategy disclosed herein below.
  • the state-of-the-art is limited by the low dynamic range of regular full scans, this is addressed by the present invention.
  • the present invention can advantageously be combined with data-independent acquisition to infer a fragment ion spectrum in silico by correlating the chromatographic elution peak of a precursor ion with the chromatographic elution peak of its corresponding fragment ions.
  • the present invention improves the signal of the precursor ions, which is limiting using state-of-the-art full scans.
  • said mass selection window(s) is/are identical with the regions defined in step (a) or are a subset of the regions defined in step (a).
  • fragmentation is effected by one, more or all of higher energy collisional dissociation (HCD); collision-induced dissociation (CID); electron transfer dissociation (ETD); electron capture dissociation (ECD); ultraviolet photon dissociation (UVPD); and infrared multiphoton dissociation (IRMPD).
  • HCD collisional dissociation
  • CID collision-induced dissociation
  • ETD electron transfer dissociation
  • ECD electron capture dissociation
  • UVPD ultraviolet photon dissociation
  • IRMPD infrared multiphoton dissociation
  • the method of the first aspect further comprises (j) determining one or more physico-chemical property(ies) other than m/z for one or more molecules of interest; (k) determining the m/z for ions obtained in step (c) from said one or more molecules of interest; and (I) identifying said one or more molecules of interest by comparing the information obtained in steps (j) and (k) with a reference data set; thereby identifying and quantifying said one or more molecules of interest.
  • Mass spectrometry provides (i) identification of species, for instance by fragmenting them, and (ii) quantification of species by their relative ion abundance.
  • the idea is to decouple both parts. Such decoupling becomes possible by relying on a reference dataset.
  • “identifying” in accordance with said preferred embodiment is effected by relying on a reference dataset
  • “quantifying” in accordance with said preferred embodiment is effected by the method in accordance with the present invention.
  • Physico-chemical properties in accordance with the present invention include the chromatographic retention time; the relative abundance of isotopes (isotopic distribution); the ion abundance of the identified peptides relative to the ion abundance of other peptides for the same protein (peptide abundance rank); the chromatographic retention time in any preceding dimension of separation (to the extent more than one separation dimension has been used); the collisional cross-section (in those cases where ion mobility spectrometry is coupled to the mass spectrometer); and the fragmentation pattern as seen, e.g., in an MS2 scan.
  • Comparing in accordance with step (I) can be done either in real-time or in the course of post-processing of the obtained data.
  • This preferred embodiment distinguishes between a reference dataset and a dataset currently under consideration. As noted above, a separate identification of analytes in the dataset under consideration is not necessary. This avoids time-consuming fragmentation scans in the mass spectrometer (assuming identification were to be performed by means of MS). On the other hand, for the purpose of generating the reference dataset, a fragment scan may be performed. This is the subject of a further preferred embodiment disclosed below.
  • FIG. 8 An exemplary implementation is shown in Figure 8. To explain further, and to increase the proteome coverage, i.e. the depth of protein identification, usually more acquisition time and more sample material is required. A common approach is to pre-fractionate complex cell lysates, either on the protein or on the peptide level.
  • the left panel in Figure 8 illustrates the pre-fractionation of a tryptic digest into 24 fractions by high-pH reverse-phase chromatography. Each fraction is separately subjected to LC-MS analysis with a standard acquisition method (total acquisition time ⁇ 1 day). This experiment yields numerous peptide identifications along with their retention time and exact mass, retention time being a‘physico- chemical’ parameter in the sense of the above preferred embodiment.
  • the goal is always to transfer identifications from an experiment (or database) with maximum depth (here termed library) into another (quantification) experiment, while the latter one is acquired with the boxcar method.
  • quantification experiment this requires only a fraction of the measurement time and sample material, while the same depth of the proteome is achieved.
  • The‘library generation’ could be done as described above, or assembling boxcar LC-MS experiments from a multitude of samples (hundreds or thousands).
  • the quantification experiment could be a‘single shot’ (LC-MS of the whole digest without fractionation, illustrated in the figure) or an experiment that includes pre-fractionation itself.
  • the‘library’ could have been built from combinations of orthogonal separation methods, with the final one being the same as in the quantification experiment.
  • said reference data set is (i) contained in a database; and/or (ii) obtained by performing steps 0) and (k) for one or more given molecules.
  • said given molecule has been identified by MS, for example by a fragment ion scan.
  • the present invention relates to a mass spectrometer comprising a mass filter, an ion store and a detector, said mass spectrometer being adapted to execute the steps of the method of the first aspect of the invention.
  • a preferred mass filter is a quadropole mass filter.
  • mass filter ion store and detector
  • said mass spectrometer further comprises a record of all acquired mass spectra.
  • the term“adapted to execute” means that the mass spectrometer has a computer program loaded, which computer program is subject of the third aspect of the present invention.
  • the present invention relates to a computer program comprising instructions to cause the mass spectrometer of the second aspect to execute the steps of the method in accordance with the first aspect.
  • Said computer program may be written in any program language. It presents the steps of the method in accordance with the first aspect in a computer readable and/or computer compilable version.
  • the present invention relates to a computer-readable medium (a) comprising instructions which, when executed on a mass spectrometer, cause said mass spectrometer to execute the steps of the method of the first aspect; and/or (b) having stored thereon the computer program of the third aspect of the present invention.
  • a preferred mass spectrometer in this respect is the mass spectrometer of the second aspect of the invention.
  • the present invention provides a computational method to quantitatively analyze data generated with the method of MS of the first aspect to the extent said method of MS comprises step (h), said method comprising: (a) aligning on a common m/z grid mass spectra acquired by performing said method of MS; (b) comparing ion abundances observed in steps (e), (f) and/or (g) of said method of MS with those observed in step (h) of said method of MS; (c) determining, from said comparing, relative transmission factors; and (d) (i) multiplying the intensities in the mass spectra obtained in step (e), (f) and/or (g) of said method of MS with the inverse of said relative transmission factors determined in step (c) of said computational method, thereby quantifying ion abundances; or (ii) quantifying ion abundances as the weighted average of all abundances observed for a given ion species in steps (e), (f) and (h) of said method of MS, the weighting factors being the relative
  • partitioning and defining at least two sets of regions in accordance with steps (a) and (b) of the first aspect of the invention and furthermore implementing the boxcar function in accordance with a preferred embodiment of the first aspect may, when effected in a real-world-setting, suffer from certain imperfections.
  • the purpose of the computational method of the fifth aspect is to account for such imperfections. Imperfections lead to ion transmissions offered by the instrument which may be lower than 100%, for example at the edges of the boxcar function (also referred to as“edge effect”).
  • step (a) allows for comparability.
  • Aligning refers to ensuring that peaks corresponding to the same ion species in different spectra coincide.
  • any reduced transmission for example resulting from the mentioned edge effects, can be determined by comparing in accordance with step (b).
  • Step (d) finally provides for the desired correction in that data obtained with less than 100% transmissions are scaled up such that they are eventually presented in a manner as if they would have been obtained with 100% transmission.
  • Items (i) and (ii) define two distinct algorithms for correction.
  • Example 4 An exemplary implementation is described in Example 4.
  • Figure 9 illustrates this procedure for a method comprising one full scan (depicted in black) and two boxcar scans (depicted in grey) in each scan cycle.
  • the total LC-MS time was 45 min, the method cycle time about 1.2 s.
  • all scans need to be aligned on a common m/z axis first (step (a)).
  • step (a) Next, all scans are summed up. In the shown experiment, this yields a summed mass spectrum for the full scan (black), a summed mass spectrum for the first set of regions and a summed mass spectrum for the second set of regions (grey).
  • a point-by- point comparison of the summed intensities for each set of regions with the full scan yields relative transmission factors for each m/z value, assuming that the transmission for the full scan is 100% at any point.
  • the transmission factors, as calculated from the summed spectra, are then applied to correct the ion abundances in every single scan from every set of regions. Having that, one can also combine all scans from each scan cycle (here: 1 full scan and 2 boxcar scans). In a preferred implementation, the weighted average of all non-zero abundances for each m/z value is calculated.
  • the weighing factors equal the transmission factors calculated above.
  • the resulting hybrid spectra can be subjected to the established post-processing procedures without further adaption (Feature detection and quantification).
  • said mass spectra are acquired with the method of MS of the first aspect, to the extent said method employs a chromatography device, and wherein said mass spectra of (e), (f) and/or (g) as well as of (h), respectively, of said method of MS are summed up across retention times as observed during chromatography in said chromatography device.
  • the computational method of the fifth aspect may comprise at any point before step (d), preferably before step (a), a step of omitting ions originating from one scan in those regions where scans overlap. This can be done by omitting ions from the scans generating the overlap. Preferably, ions at the high m/z edge from each region in one scan are omitted.
  • a smaller region at both, the high and low m/z edge of each region in both scans is omitted.
  • edges may also be omitted partially such that there still remain overlapping regions where ions of a given species will be detected and used for quantifying twice, i.e., once in the course of a first scan in accordance with step (e) of the method of MS of the first aspect, and a second time in the course of a second scan (such as a complementary boxcar scan).
  • step (h) of the method of MS the first aspect (which step (h) is a prerequisite of the computational method of the fifth aspect owing to the design of said computational method) is then dispensable, but may still be used in an optional manner.
  • a further computational method comprises (a) aligning on a common m/z grid mass spectra acquired by performing said method of MS; (b) omitting ions originating from one scan in those regions where scans overlap; and (c) quantifying ion abundances.
  • Said omitting is preferably effected as defined above.
  • Said quantifying is preferably effected by using the ions resulting from step (b) of the computational method of the sixth aspect.
  • said quantifying is effected by determining averages of the abundances of a given ion as observed in step (e) and observed in one or both of steps (f) and (h), said steps (e), (f) and (h) being steps of the method of MS of the first aspect.
  • each embodiment mentioned in a dependent claim is combined with each embodiment of each claim (independent or dependent) said dependent claim depends from.
  • a dependent claim 2 reciting 3 alternatives D, E and F and a claim 3 depending from claims 1 and 2 and reciting 3 alternatives G, H and I
  • the specification unambiguously discloses embodiments corresponding to combinations A, D, G; A, D, H; A, D, I; A, E, G; A, E, H; A, E, I; A, F, G; A, F, H; A, F, I; B, D, G; B, D, H; B, D, I; B, E, G; B, E, H; B, E, I; B, F, G; B, F, H; B, F, I; C, D, G; C, D, H; C, D, I; C,
  • Figure 1 Schematic representation of three complementing, rectangular transmission functions as applied in the boxcar scan method. The overlay of all boxcar scans yields a full spectrum over the entire m/z range as indicated in the uppermost row.
  • Figure 2 (a) Representative example of a full mass spectrum from a complex tryptic digest (b) The same spectrum as in (a), but acquired with the method of the present invention. Signal-to-noise ratios (S/N) are annotated for selected peaks and total ion injection time for each scan is depicted on top of the respective spectrum. Ion injection times and thus signal- to-noise ratios were several-fold increased in the boxcar scan. The inserts highlight a single m/z region from the acquired set of regions.
  • S/N Signal-to-noise ratios
  • Figure 3 Representative mass spectra from a tryptic digest of a human cancer cell line
  • the total AGC target value was set to 3 x 10 6 for the full scan and 1 x 10 6 for each of the boxcar scans.
  • Figure 4 Detection of isotope patterns from human plasma samples in the m/z-retention time plane with a standard full scan method (Panel a) and the method invented herein (Panel b). In the inserts, the median ion injection times per scan are illustrated as a function of m/z (white line). Panel c is a histogram of the number of potential peptide features detected with the standard method dotted line and the boxcar method solid line
  • Panels d and e illustrate the dynamic range of all detected features as a function of the retention time (d) and m/z (e).
  • Figure 5 Schematic illustration of a mass spectrometer according to the invention. Arrows indicate the direction of the ion beam.
  • Figure 6 Application of the “library approach” to single shot proteomics of mouse cerebellum (a) Number of identified protein groups per replicate and the total number of protein groups in the library, (b) The method provides consistent sampling of over 9,000 protein groups in each replicate (c) Coverage of different cellular compartments in boxcar single shots as compared with all protein groups present in the library (d) Ranked abundance of protein groups that were quantified in at least two replicate boxcar single shots. Highlighted protein groups have been previously reported to be specifically enriched in the cerebellum over other brain regions. The density distribution on the right illustrates the relative distribution of proteins associated with key cellular and neuronal functions.
  • Figure 7 Validation of the quantitative reproducibility of the MS method disclosed in here by replicate injections of a whole protein digest from a human cancer cell line. The method is cross validated with an art-established method. Very high correlations of the protein quantification indicate an excellent quantitative accuracy and reproducibility of the acquisition method as well as the post-processing workflow, including the correction for ion transmission.
  • Figure 8 Disentangling identification and quantification. Quantification is done by the method of the present invention.
  • Figure 9 Illustration of the computational method of the invention.
  • Figure 11 Label-free quantification of E.coli lysate mixed with a human cancer cell line (HeLa) lysate in 1 :2 and 1 :12 ratios (E.coli : HeLa).
  • One-sided student’s t-test returns 35% more (in total 962) significantly changing E.coli proteins at a permutation-based FDR below 0.05 for BoxCar as compared with the standard method.
  • Figure 12 Assessment of missing value rates in ten replicate 45 min analyses of HeLa digest (a) Number of unique peptide sequences quantified in specific numbers of replicates (N) with our standard shotgun method, with‘matching between runs’ (MBR) and with BoxCar in conjunction with a matching library (b) Same for quantified protein groups, (c) Completeness of the peptide quantification matrix as a function of descending peptide abundance in all three experiments, (d) Same for quantified protein groups.
  • Figure 13 Comparison of the number and dynamic range of identified features by matching from a peptide library into single shotgun with standard full scans dotted line and
  • Figure 14 Data analysis strategies with different handling of the edges of regions. In each case, only the striped aeras are considered for data analysis.
  • Option 1 includes data from both boxcar scans (also in the region of the overlap) and furthermore from the full scan.
  • Option 2 omits data from one boxcar scan in the region of the overlap.
  • Option 3 also dispenses with the full scan.
  • the method of the present invention was implemented on a hybrid quadrupole-Orbitrap mass spectrometer.
  • the resulting transmission function is referred to as a boxcar function.
  • the acquired boxcar MS spectra resemble closely the standard full scan, but the average ion injection times for each boxcar scan were more than 10-fold higher than the injection time for the corresponding full scan (Fig. 3). Closer inspection revealed that the ion injection time remained low ( ⁇ 1 ms) for boxes (i.e.
  • Figure 4 shows a two-dimensional representation of detected isotope patterns, i.e. ionized peptides, as they are eluting from the chromatographic column and detected by the mass spectrometer using the art-established full scan (panel a) and the method of the present invention (panel b). Note that, in the standard full scan, the very same ion injection time is applied across the m/z range of interest, which, compared to the method of the invention, compresses the dynamic range of the analysis and discards a large proportion of the generated ion beam.
  • the boxcar method makes more efficient use of the incoming ion beam and dedicates high ion injection times to spectral regimes with low ion current. This multiplied the number of detected peptide throughout the LC-MS experiment and increased the dynamic range by more than one order of magnitude.
  • BoxCar performed particularly well for low abundant E.coli proteins that were quantified with either low accuracy or missing values with the standard method, indicating an approximately 10- fold increased dynamic range (Fig. 11 ).
  • the intensities on the new m/z grid with common binning are calculated from the original scans as linear interpolations from the closest m/z values above and below the m/z value on the new grid.
  • BoxCar scans for each range combination as well as the full scans are summed up over the whole retention time range.
  • the summed full scan as well as the summed BoxCar scans allow us to calculate a transmission function for each BoxCar range as follows. Since the full scan summed over the whole LC-MS run, as well as the summed BoxCar scans have the same common /z grid, we can divide intensity values point wise.
  • These transmission functions are used to calculate a single high dynamic range scan, by using the transmission function as a weight for a weighted average of the full scan and all BoxCar scans from one acquisition cycle.
  • the algorithm does not require any user input but rather adapts to the experimental design, preserving full flexibility in choosing the scan range for full scans and BoxCar scans, the number of BoxCar scans as well as the number of boxes per scan. All subsequent parts of the computational workflow take these scans as input as a replacement for the commonly used MS1 survey scans.

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Abstract

La présente invention concerne un procédé de spectrométrie de masse (MS) consistant : (a) à partitionner une plage de m/z d'intérêt en au moins deux régions; (b) à délimiter au moins deux ensembles de régions, chaque ensemble de régions étant constitué d'au moins une région telle que délimitée à l'étape (a), à condition que tous les ensembles de régions, quand ils sont considérés ensemble, recouvrent ladite plage de m/z dans sa totalité; (c) à ioniser un échantillon d'intérêt et à stocker (a) un nombre défini d'ions en ce qui concerne chaque région d'un ensemble donné de régions, ce qui permet d'obtenir une ou plusieurs populations d'ions; (d) à combiner, s'il y a lieu, lesdites populations d'ions de (c); (e) à analyser la population d'ions obtenue à l'étape (c) ou les populations d'ions combinées obtenues à l'étape (d), respectivement, dans un détecteur, ce qui permet d'obtenir un spectre de masse partielle; et (f) à répéter les étapes (c) à (e) en ce qui concerne chaque ensemble de régions.
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WO2014200987A2 (fr) 2013-06-10 2014-12-18 President And Fellows Of Harvard College Enrichissement en phase gazeuse par spectrométrie de masse de type ms1 et au moyen de formes d'ondes d'isolation à encoches
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